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Öğe A Comparison of GAPDH and ACTB As Internal Control for Gene Expression Studies in Different Cancer Cell Lines(Akad Doktorlar Yayinevi, 2024) Kose, TugbaHousekeeping genes are used as internal controls to normalize the expression of target genes in gene expression studies. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and Actin beta (ACTB) are frequently preferred as housekeeping genes in gene expression studies. Due to the general alterations in the gene expression pattern in cancer cases, the selection of the appropriate housekeeping genes for these studies are challenging. In this study, we aimed to analyze the expression of the well-known housekeeping genes GAPDH and ACTB in 6 different cancer cell lines. Furthermore, the relative gene expression of the selected target gene (Tissue inhibitor of metalloproteinases 2-TIMP2) was normalized separately using GAPDH and ACTB and the obtained results were compared with each other. Finally, the stability of GAPDH and ACTB was analyzed using the in-silico tool, Bestkeeper. As a result of the study, it is found that the expression of GAPDH and ACTB were significantly different in the Jurkat (p< 0.01), MOLT4 (p< 0.05), REH (p< 0.001) and HT29 (p< 0.001) cell lines. Based on this finding, significantly different relative target gene expression values were obtained in different cell lines depending on whether the selected housekeeping gene was GAPDH or ACTB. In addition, GAPDH was found to show less variation among the samples used in all cell lines and more stability based on Bestkeeper analysis. These results support that the appropriate housekeeping gene selection, especially in cancer cell lines, may be an effective factor in obtaining accurate results for the studies in the field provide guidance to researchers.Öğe Decoding the Genetic Puzzle of Inherited Retinal Dystrophies: Novel Insights From a Turkish Cohort(Wiley, 2025) Demir, Senol; Ates, Esra Arslan; Sevik, Orkun; Sozer, Bengisu; Kose, Tugba; Sahin, Ozlem; Geckinli, Bilgen BilgeInherited retinal dystrophies (IRDs) are genetic disorders characterized by retinal pigment epithelium or photoreceptor degeneration. Advances in molecular diagnostic technologies, particularly next-generation sequencing (NGS), have facilitated the identification of disease-causing variants; however, population-specific genetic data, especially for Turkish cohorts, remain limited. This study aims to investigate the genetic profile of IRD patients in a Turkish cohort and assess the diagnostic utility of NGS-based gene panel testing. A total of 94 patients diagnosed with IRDs were included in the study. Genomic DNA was extracted from the peripheral blood of patients who met the inclusion and exclusion criteria. NGS was performed to analyze 141 genes associated with IRDs, following current clinical guidelines and utilizing up-to-date variant databases. Among the 94 patients, 97 variants were identified in 70 patients (74%). Of these, 58 variants (59.79%) were classified as pathogenic and 39 variants (40.21%) as likely pathogenic. Additionally, 28 variants (28%) were novel and have not been previously reported in the literature. Our findings demonstrate that NGS is a powerful tool for the molecular diagnosis of IRDs and emphasizes the genetic diversity of IRDs in the Turkish population. The identification of novel variants also highlights the need for continued variant curation and population-specific studies to enhance diagnostic accuracy and genetic counseling.Öğe Investigation of miR-335-5p and Its Target Gene C1QA Associated with the Complement System in Conversion from Clinically Isolated Syndrome to Multiple Sclerosis(Turkish Neuropsychiatry Assoc-Turk Noropsikiyatri Dernegi, 2025) Turk, Aysegul; Kucukali, Cem Ismail; Kose, Tugba; Karaaslan, Zerrin; Kurtuncu, Murat; Ulker, Esin Bayrali; Kahraman, Ozlem TimirciIntroduction: Multiple sclerosis (MS), an autoimmune disease, attacks the central nervous system, causing inflammation and damage. Diagnosed in four forms, many clinically isolated syndrome (CIS) patients progress to relapsing-remitting MS (RRMS). C1QA, a molecule linked to MS, might be a treatment target due to its abnormal activity in the disease. This study investigated mir-335-5p and its targeting C1QA expression as potential biomarkers for disease progression. This relationship was also evaluated from an epigenetic perspective between CIS, RRMS and control groups. Methods: Peripheral blood mononuclear cells (PBMCs) were isolated from 18 CIS, 32 RRMS, and 16 control blood samples. RNA isolation and Quantitative Real-Time PCR (qRT-PCR) were performed to detect the expression levels of C1QA and miR-335-5p, while C1QA protein levels were determined using ELISA. Results: The data revealed significant increases in both C1QA gene expression (p=0.0291) and miR-335-5p expression (p=0.0196) in CIS patients compared to controls. Although increased expression levels were observed for both parameters in RRMS patients versus controls, they did not reach statistical significance. Patients with RRMS showed lower levels of C1QA and miR-335-5p compared to those with CIS. Notably, the decrease in miR-335-5p was statistically significant (p=0.0442). No significant difference in C1QA protein levels was observed among the groups (p >0.05). Conclusion: miR-335-5p and C1QA emerge as potential biomarkers for MS progression, exhibiting significant upregulation in CIS compared to controls. miR-335-5p also shows significant downregulation in RRMS compared to CIS. These findings support the potential of miR-335-5p for distinguishing and understanding the progression of both CIS and RRMSÖğe Mechanical and biological evaluation of ?-dicalcium silicate/dicalcium phosphate-based cements: promising materials for biomedical applications(Taylor & Francis Ltd, 2025) Alshemary, Ammar Z.; Marandi, Almataz Bellah; Ali, Daver; Kose, Tugba; Dalgic, Ali Deniz; Motameni, Ali; Evis, ZaferThis study explores the synthesis and evaluation of beta-Dicalcium silicate and Dicalcium phosphate-based cements for biomedical use. beta-Tricalcium phosphate was synthesized using microwave-assisted wet precipitation, while beta-Dicalcium silicate was prepared via the sol-gel method. Composites with varying beta-Dicalcium silicate contents (20%, 30%, 40%) were formulated and characterized using X-ray diffraction, Fourier-transform infrared spectroscopy, and Field emission scanning electron microscope analyses. The 40% beta-Dicalcium silicate composite showed the highest compressive strength at 10.22 MPa. Antibacterial tests against Staphylococcus aureus revealed that gentamicin-loaded Dicalcium phosphate cement had superior properties. Cytotoxicity studies using the Osteogenic sarcoma cell line revealed that the beta-Dicalcium Silicate /Dicalcium Phosphate composites supported better cell viability compared to pure Dicalcium phosphate cement, with the 20% beta-Dicalcium silicate /Dicalcium phosphate composition being the most effective in promoting cell growth. These findings suggest that beta-Dicalcium silicate /Dicalcium phosphate composites hold promise for biomedical applications.
